Sequence
atgc intronic sequence ATGC exonic sequencegtaagacttaatttttggtactcttttgggacctacttgacattcattttgcactaacaatcattgaattgtataagatctaaggctatgcataattgttttagaccataatccaaggtgttctagaaatcaattgtttctgtactttcttgtcattatgcacttatactgtattacattctcctggtttcagGTCAAATTTTCTTGGCACCAAGTTTATAATTTATGATACACAACCTCCCTACCACAATGCTATGCTGTCTCCACCTGGCCGCAGCCGTAGGTTTTCAAAA
Basic information
species | Glycine max |
transcript | GLYMA20G30660.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G30660.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g64700.2 (Oryza sativa), 3'ss of exon 5
gtaagacttaatttttggtactcttttgggacctacttgacattcattttgcactaacaatcattgaattgtataagatctaaggctatgcataattgttttagaccataatccaaggtgttc-tagaaatcaattgtttctgtactttcttgtcattatgcacttatactgtattacattctcctggtttcagGTCAAATTTTCTTGGCACCAAGTTTATAATTTATGATACACAACCTCCCTACCACAATGCTATGCTGTCTCCACCTGGCCGCAGCCGTAGGTTTTCAAAA
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-----------------------------------------------------------------------------------------------------------gtaatt-atcatgttcattgaagatggttattttccattttgcttgtttcataatatataaacccta--gcactgtcat--ttccagGTCAAATTTCCTTGGCACAAAATTTATAATTTATGACACACAGCCCCCTTACAATGGGGCTGTAGTCCCTCACGTCGGAAGGACCAGCAAGAGATTTAAC
upper sequence: GLYMA20G30660.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 3
gtaagacttaatttttggtactcttttgggacctacttgacattcattttgcactaacaatcattgaattgtataagatctaaggctatgcataattgttttagacc-ataatccaaggtgttctagaaatcaattgtttctgtactttcttgtcattatgcacttatactgtattacattctcctggtttcagGTCAAATTTTCTTGGCACCAAGTTTATAATTTATGATACACAACCTCCCTACCACAATGCTATGCTGTCTCCACCTGGCCGCA---GCCGTAGGTTTTCAAAA
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----------------------------------------------------------------------------tatttcaggtca---atttttgttttaagcctataatctagtttgtgtt---cataaattactctctatctgtctcaaaatt------------tgtttgtcctcccccttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATACAATGGTTCTCAACTCTCCCCACCTGGCCGAACGAGCCGGAGGTTCTAC---Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|21888011|gb|BQ741224.1|BQ741224EST: GATGCAGATAACATATCGAGATCTAGTAGTACTTACATTGGAAAACTGAG GTCAAATTTTCTTGGCACCAAGTTTATAATTTATGATACACAACCTCCCTA
genomic: GATGCAGATAACATATCGAGATCTAGTAGTACTTACATTGGAAAACTGAGgtaagactta ... ctggtttcagGTCAAATTTTCTTGGCACCAAGTTTATAATTTATGATACACAACCTCCCTA
EST:
gi|9901142|gb|BE610110.1|BE610110EST: GATGCAGATAACATATCGAGATCTAGTAGTACTTACATTGGAAAACTGAG GTCAAATTTTCTTGGCACCAAGTTTATAATTTATGATACACAACCTCCCTA
genomic: GATGCAGATAACATATCGAGATCTAGTAGTACTTACATTGGAAAACTGAGgtaagactta ... ctggtttcagGTCAAATTTTCTTGGCACCAAGTTTATAATTTATGATACACAACCTCCCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgtactttcttgtcattatgcacttatactgtattacattctcctggtttcagGTCAAATTTTCTTGGCACCAAGTTTATAATTTATGATACACAACCTCCCTACCACAATGCTATGCTGTCTCCACCTGGCCGCAGCCGTAGGTTTTCAAAA
cattctcct CT-rich tract
tattacatt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagacttaatttttggtactcttttgggacctacttgacattcattttgcactaacaatcattgaattgtataagatctaaggctatgcataattgttttagaccataatccaaggtgttctagaaatcaattgtttctgtactttcttgtcattatgcacttatactgtattacattctcctggtttcagGTCAAATTTTCTTGGCACCAAGTTTATAATTTATGATACACAACCTCCCTACCACAATGCTATGCTGTCTCCACCTGGCCGCAGCCGTAGGTTTTCAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG